RNA interference is one of the effective emerging anti-viral strategies to inhibit virus infection in cells. In this study, small interfering RNAs (siRNAs) generated against various sites of West Nile virus (WNV) genome was used to target and destroy WNV transcripts. Two different versions of vectors (for transient and stable expressions) were constructed and their efficacies in silencing WNV replication were compared in this study. A combination of techniques such as molecular (real-time PCR), proteomics (Western blot analysis), microscopy (immunofluorescence and transmission electron miscroscopy) and plaque assays was employed. Stable expression of siRNAs showed a greater promise in silencing WNV replication than the transiently expressing siRNAs Continuous expression of siRNA is a simple and effective way to combat WNV infection and the machinery of RNA inferring mechanism that is present in the nature can be exploited to target against other flavivirus, hence preventing infections.